rs2181033

Variant names:

• chr9-114935551-A-G
• rs2181033
• ENST00000648852.1:n.198+13953A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648852.1(DELEC1):​n.198+13953A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 152,080 control chromosomes in the GnomAD database, including 9,287 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.34 (9287 hom., cov: 32)
• Consequence: DELEC1 ENST00000648852.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.628

Genes affected

DELEC1 (HGNC:23658): (deleted in esophageal cancer 1) The function of this gene is not known. This gene is located in a region commonly deleted in esophageal squamous cell carcinomas. Gene expression is reduced or absent in these carcinomas and thus this is a candidate tumor suppressor gene for esophageal squamous cell carcinomas. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DELEC1	ENST00000648852.1	n.198+13953A>G		intron_variant	Intron 2 of 5
DELEC1	ENST00000649565.1	n.226-34033A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51831 AN: 151962 Hom.: 9277 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.343

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.341 AC: 51864 AN: 152080 Hom.: 9287 Cov.: 32 AF XY: 0.344 AC XY: 25582 AN XY: 74334

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.348

Alfa AF: 0.371 Hom.: 4994

Bravo AF: 0.339

Asia WGS AF: 0.379 AC: 1313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.71

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2181033; hg19: chr9-117697831;